ABSTRACT Sarcoidosis is a granulomatous inflammatory disease often dubbed a “medical mystery” yet significantly understudied. While it is known that sarcoidosis likely involves host genetic susceptibility and an innate and adaptive immune response to infectious, organic or inorganic agents, the mechanisms by which granulomas form and the determinants of severity and manifestation of disease remain elusive. Over the past several years, our team has led the charge to define the role of genetics in sarcoidosis. Specifically, under our current funding, we have published 13 papers with 3 more soon to be submitted describing genes for susceptibility, severity, ancestry specific and organ-specific effects. However, the mechanism(s) by which associated genetic variants influence sarcoidosis are still largely unknown. Our proposal will close this knowledge gap by characterizing functional variants and the tissue(s) in which they operate by 1) identifying differentially expressed (DE) genes in granulomatous tissue and blood, 2) characterizing the expression of DE and previously associated genes by specific cell type, 3) identifying tissue or cell-specific eQTLs for DE and previously associated genes, 4) creating clinical profiles of patients carrying risk alleles and 5) replicating our findings in an independent cohort. Specifically, in Aim 1, we will identify novel candidate genes and their most likely causal variants to be investigated in our future mechanistic studies of sarcoidosis susceptibility and persistence via DE analysis of RNA sequencing data of whole blood from both EA and AA sarcoidosis patients and matched controls AND DE analysis of granulomatous tissue from a subset of these same patients compared to healthy tissue. Additionally, we will perform eQTL analysis using the transcriptomic data from blood and tissue described above and ancestry-informative genome-wide genotyping data. In Aim 2, we will define the cell subsets in which the most likely causal variants operate and identify novel cell-specific effects by DE analysis of RNA sequencing data from blood-derived single cells in our cohort of EA and AA cases and matched controls. In order to identify cell-type specific eQTLs, analysis of the genotype and single cell transcriptomic data will also be performed. Finally, in Aim 3 we will replicate our list of candidate genes, their most likely causal variants and the specific cell type in which they influence disease using blood, tissue and single cells from a cohort of patients recruited based on the demographic and clinical criteria that are associated with our causal variants. Our work will be greatly facilitated by the extensive genotype, clinical and environmental data on our existing cohort AND the recently established Sarcoidosis Research Unit from both of which we have strong preliminary data to support the studies proposed herein. In summary, when this grant is complete, we will know the likely causal variants, the tissue and cell-...